Thanks Scott,
To answer a few of your questions:
No, ORNL does not have a supported amber installation. We have a site
license for amber14 only, which is why no upgrade. If we want to use it we
have to download it ourselves and build.
Yes, I am very familiar with the compiling procedure at ORNL and I have
submitted a help ticket, but currently no one with a good amount of
compiling experience here can figure out how to deal with this problem.
I have the serial build in a completely different folder, and I ran the
parallel build complete anew, from a different login, even.
Yes, I do need parallel executable, as the reason we are trying to use
amber is for the DFT-MD for a larger small system.
I will check the serial tests. That is strange.
Thanks again,
Ada
On Fri, Jan 13, 2017 at 2:35 PM, Scott Brozell <sbrozell.rci.rutgers.edu>
wrote:
> Hi,
>
> The most likely possibilities are probably:
> 1. broken parallel tools;
> 2. conflicting serial and parallel tools;
> 3. residual conflicting amber files between the serial and parallel builds.
>
> The apparent first error:
> > /usr/bin/ld: reader.o(.text+0x5a): unresolvable R_X86_64_PC32 relocation
> might be fixed with compiling options like -fpic.
>
> But my advice is to take a step back and tackle these bigger picture items:
>
> Doesn't ORNL have supported amber installations ?
> Did you read the ORNL documentation on installing software, etc ?
> Did you ask them for help ?
> Do you need parallel amber executables ?
> When will you upgrade to amber 16 ?
> Double check your serial tests - i haven't seen all passing tests in
> amber for at least a decade.
>
> If you still need help from us after investigating those then send
> verbose and verbatim details: compiler names, versions, -show output,
> your config.h s, the redhat-release, the complete build logs, etc.
>
> scott
>
> On Fri, Jan 13, 2017 at 12:52:40PM -0500, Ada Sedova wrote:
> > I am trying to build amber14/amberTools on RHEA, an OLCF (ORNL) commodity
> > cluster, with dual Intel® Xeon® E5-2650 CPUs, which uses modules.
> >
> > The build was successful on the same system in serial, and all tests
> passed
> > after building.
> >
> > However, when trying to build with mpi, I am exiting the make install
> from
> > the following folder:
> >
> > make[2]: Entering directory
> > `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/src/cifparse'
> >
> > flex -t cifparse.l | sed 's/yy/cifp/g' > lex.cif.c
> >
> > /ccs/home/adaa/AMBER/amber14/bin/yacc -v -d cifparse.y
> >
> > make[2]: Leaving directory
> > `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/src/cifparse'
> >
> > make[1]: Leaving directory
> > `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/src'
> >
> > with the following error:
> >
> > main.o: In function `create_file_names':
> >
> > main.c:(.text+0x607): warning: the use of `mktemp' is dangerous, better
> use
> > `mkstemp'
> >
> > /usr/bin/ld: reader.o(.text+0x5a): unresolvable R_X86_64_PC32 relocation
> > against symbol `cache'
> >
> > /usr/bin/ld: reader.o(.text+0x6c): unresolvable R_X86_64_PC32 relocation
> > against symbol `cache'
> >
> > /usr/bin/ld: reader.o(.text+0x73): unresolvable R_X86_64_PC32 relocation
> > against symbol `cache'
> >
> > /usr/bin/ld: reader.o(.text+0x84): unresolvable R_X86_64_PC32 relocation
> > against symbol `cache'
> >
> > /usr/bin/ld: reader.o(.text+0x5b1): unresolvable R_X86_64_PC32 relocation
> > against symbol `cache'
> >
> > /usr/bin/ld: reader.o(.text+0x5c9): unresolvable R_X86_64_PC32 relocation
> > against symbol `cache'
> >
> > /usr/bin/ld: reader.o(.text+0x5eb): unresolvable R_X86_64_PC32 relocation
> > against symbol `cache'
> >
> > /usr/bin/ld: reader.o(.text+0x60d): unresolvable R_X86_64_PC32 relocation
> > against symbol `cache'
> >
> > /usr/bin/ld: reader.o(.text+0x62f): unresolvable R_X86_64_PC32 relocation
> > against symbol `cache'
> >
> > /usr/bin/ld: reader.o(.text+0x651): unresolvable R_X86_64_PC32 relocation
> > against symbol `cache'
> >
> > /usr/bin/ld: reader.o(.text+0x669): unresolvable R_X86_64_PC32 relocation
> > against symbol `cache'
> >
> > /usr/bin/ld: reader.o(.text+0x68b): unresolvable R_X86_64_PC32 relocation
> > against symbol `cache'
> >
> > /usr/bin/ld: reader.o(.text+0x6ad): unresolvable R_X86_64_PC32 relocation
> > against symbol `cache'
> >
> > /usr/bin/ld: reader.o(.text+0x6cf): unresolvable R_X86_64_PC32 relocation
> > against symbol `cache'
> >
> > /usr/bin/ld: reader.o(.text+0x1590): unresolvable R_X86_64_PC32
> relocation
> > against symbol `cache'
> >
> > /usr/bin/ld: reader.o(.text+0x15f7): unresolvable R_X86_64_PC32
> relocation
> > against symbol `cache'
> >
> > /usr/bin/ld: reader.o(.text+0x1785): unresolvable R_X86_64_PC32
> relocation
> > against symbol `cache'
> >
> > /usr/bin/ld: reader.o(.text+0x194f): unresolvable R_X86_64_PC32
> relocation
> > against symbol `cache'
> >
> > /usr/bin/ld: reader.o(.text+0x1967): unresolvable R_X86_64_PC32
> relocation
> > against symbol `cache'
> >
> > /usr/bin/ld: reader.o(.text+0x1976): unresolvable R_X86_64_PC32
> relocation
> > against symbol `cache'
> >
> > /usr/bin/ld: reader.o(.text+0x1b70): unresolvable R_X86_64_PC32
> relocation
> > against symbol `cache'
> >
> > /usr/bin/ld: reader.o(.text+0x1c41): unresolvable R_X86_64_PC32
> relocation
> > against symbol `cache'
> >
> > /usr/bin/ld: reader.o(.text+0x1ffb): unresolvable R_X86_64_PC32
> relocation
> > against symbol `cache'
> >
> > /usr/bin/ld: reader.o(.text+0x2002): unresolvable R_X86_64_PC32
> relocation
> > against symbol `cache'
> >
> > /usr/bin/ld: reader.o(.text+0x2659): unresolvable R_X86_64_PC32
> relocation
> > against symbol `cache'
> >
> > /usr/bin/ld: reader.o(.text+0x2693): unresolvable R_X86_64_PC32
> relocation
> > against symbol `cache'
> >
> > /usr/bin/ld: reader.o(.text+0x26ac): unresolvable R_X86_64_PC32
> relocation
> > against symbol `cache'
> >
> >
> > yacc:3249 terminated with signal 11 at PC=40abac SP=7fff87123600.
> > Backtrace:
> >
> > /ccs/home/adaa/AMBER/amber14/bin/yacc[0x40abac]
> >
> > /ccs/home/adaa/AMBER/amber14/bin/yacc[0x40ce6b]
> >
> > /ccs/home/adaa/AMBER/amber14/bin/yacc[0x404dfd]
> >
> > /lib64/libc.so.6(__libc_start_main+0xfd)[0x7eff172bed1d]
> >
> > /ccs/home/adaa/AMBER/amber14/bin/yacc[0x400ea9]
> >
> > make[2]: *** [cifp.tab.c] Error 1
> >
> > make[1]: *** [parallel] Error 2
> >
> > make: *** [install] Error 2
>
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Received on Fri Jan 13 2017 - 12:30:02 PST
